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Wednesday, June 10, 2015

101 ancient Eurasian genomes (Allentoft et al. 2015)

It'll take me a while to digest all of the information in this massive new Allentoft et al. paper. But I've already noticed that, just like in Haak et al. 2015, the Yamnaya samples are again from the eastern half of the Yamnaya horizon. This time, however, not all of the Yamnaya individuals carry Y-haplogroup R1b; one of the five samples belongs to Y-haplogroup I2a (see here).

So I'm wondering what more westerly Yamnaya sites will reveal in the future, considering the predominance of Y-haplogroup R1a among the Corded Ware individuals sampled to date, and the close genome-wide relationship between the Yamnaya and Corded Ware?

Abstract: The Bronze Age of Eurasia (around 3000–1000 BC) was a period of major cultural changes. However, there is debate about whether these changes resulted from the circulation of ideas or from human migrations, potentially also facilitating the spread of languages and certain phenotypic traits. We investigated this by using new, improved methods to sequence low-coverage genomes from 101 ancient humans from across Eurasia. We show that the Bronze Age was a highly dynamic period involving large-scale population migrations and replacements, responsible for shaping major parts of present-day demographic structure in both Europe and Asia. Our findings are consistent with the hypothesized spread of Indo-European languages during the Early Bronze Age. We also demonstrate that light skin pigmentation in Europeans was already present at high frequency in the Bronze Age, but not lactose tolerance, indicating a more recent onset of positive selection on lactose tolerance than previously thought.

I see the bar plots in Fig.6 I'm still trying to figure out where the individuals come from.

In any case, Remedello I is definitely Neolithic and looks like a lot like Sardinian and Trelles individuals, which honestly is not surprising.

Again, every swinging **** Bell Beaker was mixed with Corded Ware folk. There is no island and no continent where they weren't mixed, and above all, Central Europe where the only BB genomes come from. Even the earliest Portuguese Beakers probably had Peninsular Corded influence. So I'm not quite sold on BBC and CWC being two peas in a pod.

In other words, the lesser Yamnaya or ANE like influence so far detected in BB, more than likely is because they are at least half Battle Axe in their ancestry. More than any place, this would be especially true on the Elbe and Mittel-Saale

More samples of bell beakers and they all come back r1b. Also, we now have an r1b sample in Corded Ware even though they mostly come out r1a.

Also, here is what they say about androvono "The enigmatic Sintashta culture near the Urals bears genetic resemb- lance to Corded Ware and was therefore likely to be an eastward migration into Asia. As this culture spread towards Altai it evolved into the Andronovo culture (Fig. 1)"

also, once again we have r1b being dominant in yamnaya. I think its getting clear that yamnaya were r1b, their was a minor input of yamnaya into the closely related corded ware, and corded ware then moved east and replaced most of the r1b on the steppe along with spreading IE culture eastwards.

Also, Bell beaker is not corded ware derived but yamnaya derived, albeit closer to farmers than the yamnaya themselves which is probably due to mixture with locals and the fact that bell beaker comes from the western yamnaya.

Fascinating! It will be important to determine whether the R1b among BA Armenians is Z2105 or not. The R1b is well before the Armenian language, but BA Armenia has a large "Teal" component like Yamnaya. We should also determine if the BA Armenian is V13 or M123--makes a huge difference. The Iron Age J2s--J2a in Altai and Russia and J2b in Armenia fit with a later J2 expansion, like J2a1b in BR2 Hungary. BA Armenians do appear to be a palimpsest of Neolithic farmers sharing with EN Europeans and contemporary Sardinians and Chalcolithic N Italians.

@Mike ThomasNot really, most Scythian samples still were predominantly R1a. Scythians were nomads who migrated quite much and during their migrations they mixed with other populations and picked their dna/y-DNA. I would be even not surprised if they found Y-DNA L or G in the iron age steppe originating from Saka tribes who spent some time in South Central Asia and migrated back.

"Using D-statistics, we find that Corded Ware and Yamnaya individuals form a clade to the exclusion of Bronze Age Armenians (Extended Data Table 1) showing that the genetic ‘Caucasus component’ present in Bronze Age Europe has a steppe origin rather than a southern Caucasus".

There is no replacement. The I2 is typical of neolithic farmers, and it is a lineage that comes from the mesolithic. This sample from Italy is close to Sardinians and thus neolithic farmers. Nothing strange.

The Iron Age Russian samples are from Southern Siberia and have affinities to modern Siberians despite being J2. There's also J2a in Iron Age Altai which is broadly similar. Greek relation seems unlikely, but modern Central Asian J2 might be worth a comparison.

Nice summary in the supplementary material (BAE= Bronze Age Europeans)

"In summary, our results suggest the following interpretations:- Predominantly West Eurasian ancestry for BAE, with the exception of some later BA individuals from Asia, which show influence of ancestry related to present-day Siberians- A gradual decrease in West-Asia / Neolithic farmer related ancestry from Southern and Central BA Europeans towards the North, which is also present in Armenians but absent from the Northern Caucasus (Yamnaya).- An opposing gradient in Caucasus / steppe related ancestry, maximized in the Yamnaya and distantly related to Native Americans. Possibly due to the presence of MA1-related ancestry in the Northern Caucasus.- A genetic link between the Kalash and the steppe through Yamnaya-related people. - Native American-related ancestry in the Okunevo, possibly due to shared ancestry with paleolihic hunter-gatherers from Mal’ta."

Iron Age Altais and Iron Age Russia full of J2. "acculturated other groups" my a$$ :D

This is clearly the geographic distribution of Scythians.

I said it in the past and will say it again. Scythians were a mix of R1a*, J2a and some other Haplogroups such as R1b/R2 LT*, G just like any other Indo_Iranic tribe. It gets obvious if you look at the Haplogroup distribution of modern Indo_Iranic speakers. It can't be "acculturated" Haplogroup if it exists among all branches of the Indo_Iranic family.

Stating the obvious - this study is great Excellent sample set, and makes well substantiated conclusions

It shows clearly what I've been suggesting - whilst the process of PIE began in the early Bronze Age; it was an ongoing affair- as late Iron Age still unfurling. And there were clearly more complex admixture processes than single-origin ones

@KurtiScythians were Post-PIEs so non-R1 lineages among them are not surprising in any way. Anthropological studies showed that southern Saka resembled modern Pamiri and were different from the more "european-like" and more northern living Iranians. Scythians in the Caucasus resembled modern Caucasians to a large extent also and the Siberian Iranians were quite siberian/uralic shifted if I am not wrong. So they were not just the descendants of Proto-Indo-Iranians even when they were extremely close to Proto-Indo-Iranians.

If it was due to "colinies" in East Europe, how are we going to explain the appearance in Iron Age Altais? Obviously no Greek colonies. Both places known as Scythian settlements. When the Indo_Iranic people formned and especially when the Scythian formed. The must have belonged to various Haplogroups. We know from a study that the Alans from East Europe were mostly G2a as example.

A reference to CT, at last!Let's keep in mind that PIE is a reconstruction, so there could be different "dialects" of what we call PIE... I can't possibly believe that I can get into a time machine and arrive to a time and place where they speak PIE just as it was reconstructed.

Well, there certainly appears to be a radiation of J2 during the mid-late Bronze and iron ages, when PIE was being consolidated in the places where it is first attested- Greece, Anatolia, Indo -Iranian lands, Italy..../

Given that they make the connection that the success and westward expansion of the Yamnaya is derived from a cultural/technological package learned from Mesopotamia it would seem to imply that the "teal" component in the Yamnaya was input from ancient Mesopotamia itself.

"If J2 expanded in Central Asia only during the Iron Age, then it wasn't a feature of the earliest Indo-Iranians.

Come on."

It must have been, Otherwise you would expect this Haplogroup to lack in some branches.

Since it is found among all Indo_Iranian branches in significant percentage it must be a native part of them.

There is no other explanation for that.

Just as example if you have green eyes, all your siblings have green eyes, and your niece (the daughter of your brother) has green eyes too. What is more likely, that she inherited this from your bro or his wife?

J2 is strong in all Indo_Iranians even those living isolated in the Pamir Mountains, heck even Uygurs in West China.

@KurtiNot all are rich in J2 Pashtuns have just around 5% of it. All Indo-Iranians(except of some Indians) today populate regions where Neolithic Farmers lived once so they have a similar near eastern-related substrate. Andronovo/Sintashta will have no J2 maybe I2a, N or R1b but certainly no J2.

Davidski, I agree with you that Corded Ware (expanding to the west) and Andronovo (to the east) spoke languages derived from what was spoken in Yamna, whatever language it was. My comment was about CT being "too large" (in population, I assume) to be the PIE homeland, and that maybe the CT people (and Sredny Stog too) could have spoken different dialects or variations of what we call PIE.Following Mallory, I don't think PIE was the language of a nomadic pastoralist population, it has too many agricultural and architectural terms for nomads. But I haven't found a fully convincing theory yet.

if old near eastern was E1 (of one or more kinds) and they were mostly replaced by X from somewhere adjacent to the Himalayas who moved into the near east and became a new near eastern (and then also moved on from the near east into Europe) and who also moved onto the steppe east of the Caspian mixing with the steppe R1 component to become incorporated into PIE and then some of that R1b PIE moved into Armenia then you might end up with

Yamnaya = steppe + new near easternArmenian = yamnaya + old near easternIraqi Jews = old near eastern + new near eastern

mostly messin' but just thinking about how multiple populations could be 50% similar to each other by being 100% on one branch of admixture and 0% on another.

"Given that they make the connection that the success and westward expansion of the Yamnaya is derived from a cultural/technological package learned from Mesopotamia it would seem to imply that the "teal" component in the Yamnaya was input from ancient Mesopotamia itself."

Does that follow? Couldn't it simply mean they had something to trade (horses, copper?) and the thing(3) they had to trade were responsible for the success and westward exapnsion?

I haven't been following the near eastern admixture in yamnaya too closely but has this paper helped to sort out the matter of where that component came from and how it relates to the typical, sardinian like, farmer ancestry in europe?

Based on a quote mike picked out it sounds like that might have been the CT culture. Mike, what was the time frame for the CT input into the steppe populations?

Colin There is evidence for exchange as early as 5000 BC (ie pre-pre-Yamnaya period). But it apparently poured in just prior and c. 3000 BC, as C-T disintegrated (ie spread out all over central, eastern (esp. steppe) & Southeastern Europe.

If the later is true then they may be a candidate for the "new neolithic" in yamnaya. Are you sure it was 3000bc and not a little later. Because at 3000bc it would be difficult to homogenize such a component across the yamnaya horizon but possible. Any later and we are no longer talking about a group that fused with the yamnaya, but invaded the already established yamnaya.

Exceptions confirm the rule. Look at all the Indo_Iranian tribes around them. So what can the Pashtuns prove anyways. Thats pocking for mistake in an almost perfect scenario, Ossetians are the only Indo_Iranian group with close to 2% R1a. Claiming R1a is not part of the Indo_Iranian tribes would be ridiculous.

Also all DNA studies I have seen on Pashtuns shows at least 8% J2. But than even 5% is significant.

Here's a comment by David Anthony on the southern admix in the Yamnaya sampled to date. I think it's a reasonable assessment for now.

"On the "Caucasian" element in Yamnaya: Sasha Khokhlov in Samara and Sasha Kozintsev in St Petersburg, both biological anthropologists, have described a narrow-faced skull type that is often labeled 'Mediterranean', but both have documented that this type existed as a native element in the steppes at a very early era, and it was not really classic 'Mediterranean'. This type could represent a southern steppe population that already existed in the Mesolithic, linked to Mesolithic populations in the North Caucasus. The genetic element in Yamnaya that seems to come from a Caucasian population was present earlier at the Eneolithic Khvalynsk cemetery. This is not yet published. The mysterious Caucasian element is about 25% of the ancestry of Khvalysnk, but it rises to 50% of the ancestry of Yamnaya. Perhaps the additional increment of Caucasian genes came through increased marriage between Maikop and steppe people after Maikop introduced wheeled vehicles to the steppes (???)."

Well, yes it might have extended to later, of course. In fact, most likely in the first quarter to mid second Mill BC. But I agree with David, Im not suggesting CT expansion reached all the way to north central Asia.

Low level of LP implies dramatic rate of increase in north western Europe.

If it was selection pressure then you'd think selection pressure on that scale ought to have spread further in southern and eastern Europe by now unless the advantage was specific to the northwest region in some way i.e. climate i.e. crop yields i.e. calories.

I don't know what to say. Can you see the speadsheet at all? Anyways, here's the Y DNA. I don't know how many samples successfully found their Y DNA haplogroup. I just listed the number of males from each group.

The I1, R1b(U106, L238, DF19, DF99?), and R1a together in Late Neolithic/Bronze age Sweden/Denmark support the idea proto-Germanic developed around south Scandinavia, northern Germany, and the Netherlands. I1 hasn't been found anywhere else, except Neolithic Hungary.

They must be. I checked Felix's site. He hasn't made any posts about work on Alentoft genome. BTW, the Bronze age Montengero man is clustering in SouthEast Europe. Almost all LN/BA are in central Europe. Not consistent with Haak genomes.

actualky Karl, they intimate that all this was set off by other social and demographic mechanisms. So it wasnt "first from the steppe". The steppe movements wer secondary; and there were other tertiary and quaternary movements

Obviously. But you could say the same thing back to the beginning of time. Actually... this was just part of a mass migration from Africa.

I was only referring to Marnie's particular concern about the directions that people were moving within this time period. Saying that Indo-European languages didn't spread to Europe via a mass migration from the Steppe is looking quite absurd with the data at hand.

Although I was among the very few anticipating emergence of J2 linages among these new samples, now that we eventually have them, I really do not know what to make of them!! Their location is absolutely surprising to me. I see people rushing to link these J2 samples with the Scythians and others with Neolithic farmers. I prefer to remain undecided at this point. What puzzles me is the high frequency of J2 in Crete and Cyprus (around 25-30% in both islands). If J2 was a Central Asian haplogroup, you would need a massive migration from there into these two islands. The same applies to the scenarios putting the origin of J2 somewhere in the Caucasus. I am not sure if we can support such migrations archaeolgically. Probably not. We can support a migration from Anatolia to Cyprus (and maybe Crete) during the early Bronze age however. What we cannot be certain is whether J2 was already present in the Eastern Mediterranean islands before the Anatolian migration, or whether this migration brought the J2 along.

Another interesting finding for me is the E1b1b in BA Armenia. I beleive if we find out the subclade of this haplogroup (M123, V22, V13?) it will reveal tons about the presence of E1b1b in ancient southeast Europe. My guess is that this will be a V13, but I have noticed people doubting this. I do not know why..

I still need to read the paper carefully, but one thing no one has commented about: The Afanasievo samples seem to be almost exactly like the Yamnaya ones. Yet, they are contemporary (or Afanasievo might actually be older). And they are from places some 2000-3000 Km. away.

Isn't this a bit odd, when Yamnaya was a mix of 2 quite different populations? Did the exact same mix of the exact 2 different populations happen at the same time in such distant places? Or once the mixing finished (after a 1000 years process) this new population moved really fast? And if so, in which direction, Yamnaya->Afanasievo or the other way around?

Alberto,'' Yamnaya->Afanasievo or the other way around?''Interesting i actually suggested more about homogeneous population between the Central Asian and East European rather than movements from A->B or B->A , if we had aDNA from neolithic that would have been gold...

@KrefterThanks, that's great! Where did you find this info?? So M123? That's intriguing.. My first thought then is that M123 might have been a (minor) subclade of the Neolithic diffusion, at least the difussion from the Levant to North Anatolia. I am not saying that this is a fact. Still need to get my head round it..

@MikeI see your point about island populations, however note that both Cyprus and Crete are large islands with nearly 1M population each. Yes bottlenecks and genetic drifts are likely, but on the other hand it may happen that they escape some of the migrations affecting the mainland. Look at Sardinia for example..

The Afanasievo samples are all radiocarbon dated from ~3100 to ~2800 BC (give or take a century or two), while these Yamna samples (of which 3 are dated) have central dates of ~3000 to ~2500 BC, give or take about 350 years (!). So these Yamna samples are probably a little younger than the Afanasievo ones. The Haak et al Yamna samples, OTOH, are almost exactly the same age range as these Afanasievo ones.

"'Id say that both the ancestors of the Afanasievo people and the Tarim Basin mummies, who might well have been one and the same, left the European steppe before Yamnaya proper came into being.

I'm betting they were the Repin people, who also helped to form corded ware .."

Good initial point Alberto. The Afansievo is at least contemporary, if not older. And whilst possible, I don't buy the Repin explanation, for the obvious reason that they were at best incipient pastoralists; and lacked the social -cultural and demographic means to achieve such a mugration feat.

Nirj:Of course we need DNA from the rest of eurasia. To me, the cumulative data suggests that the northern most areas were susceptible to massive population fluctuations. By the BA a massive chunk of northern west eurasia was more or less homogeneous, **geneticaly**. But does this = PIE ??!

Dave True First of all, that study is sloppy as it lumps half of west eurasia as "Yamnaya", as well as very early forms which are too premature to call Yamnaya. For now, I'm taking Rassamakins word on chronology; and whatever the case, the secondary nature of Yamnaya phenomenon is clear to eveyone in the know; including the learned authors of the study we're presently discussing

My only critique is , without actual neolithic samples, we're no closer to solving the same debates we've been having for 3 years.

Yes, the tarim mummies might well have been european, indeed, or at least partly so.

@AramSurely makes more sense, but where do you base these conclusions regarding the haplogroups? I am not trying to refute you, but we really need to have some credible data on the Y-hgs soon to avoid this confusion, as we are all trying to run to conclusions, with data not yet entirely confirmed (to clarify I am just talking about Y-hgs, not the autoosmal data)

This is the regional distribution of R1b among the modern Armenian populations.https://drive.google.com/file/d/0BwiYFZ1GMcZLWE1iMW02Qk9BUkE/view?usp=sharing

Clearly the highest frequency is in the East. Remembering that Talyshs, north Iranian Gylaks, Iranian Lurs and also Lezgins are also high in R1b so we can have the approximate idea from where Armenian R1b came. It is highly improbable that it moves from Yamna to Balkans crossed all Anatolia and Arm. Highlands and had a founder effect in Eastern Armenia and Iran.

Thanks Aram. Are these supplementary tables from the paper? I still did not have the chance to read the whole paper with all the supplementary material..

Regarding what you mention on the distribution of R1b in the Armenian territory, I have noticed from the Cinnioglu et al paper, that the highest frequency of R1b in Anatolian Turks is in the North Central (area 2), followed by South Central (area 6). What would you make of this regarding the direction of R1b migrations to/from Anatolia?

MikeEverything is possible. But such a movement means that R1b came from Balkans to East Armenia/Iran circa 2000 BC just before the establishment of Hittite empire. so generaly this does not change much to the fact that R1b in LBA Armenia has IE origin and not a Hurrian. What some people try to show.

But the most probable route remains from East to West trough north Anatolia.

I don't know where R1b came from to Armenia. On the basis of present evidence, it could be east or north. But I am more sure that it wasn't brought by "The Armenians", beuuase such people didn;t exist 3000 BC. IN fact, Im not even sure that R1b was exclusively even PIE at all

I don't think I ever said that Armenians existed in 3000 BC. What I am saying is that in the current stage of our knowledge the R1b in Northern parts of West Asia is most probably a solid marker of IE presence. If it is not the case. And R1b has no any correlation with IE in Northern West Asia then we can start to make other assumptions and speculations about other Hgs or even non-Steppe origin of PIE.

p.s. In my opinion the R1b is a marker of IE presence in Northern West Asia. If Central Asian origin of this R1b is shown I will change my mind.

Alexandros Yes that table is from the paper. The map of R1b frequency is from elsewhere.

My opinion about the movement of R1b is like this. It has a Steppe origin. It's highest frequencies are close to Caspian and Black sea. This mean he was moving by the costline or rivers. So if the origin is the Yamna and not a place like Turkmenistan, then it moved South to Caucasus later moved to Greece trough North Anatolia. The Balkanic route is also possible but it should be early rather than late. Two different routes are also possible but in this case we should find some differences in North Iranian R1b-Z2103 subclades and Greek ones.

I actually agree with what you're saying. The connecting link is Majkop, via Daghestan.. What I'd like to see is aDNA from the Nth Caucacus and Ukraine. Is it also R1b, or R1a, or both ? But so far, R1b and R1a seem well separated.

I'm not going to take the risk of damaging my laptop. Is anyone else able to do it? BTW, a Yamnaya and Armenian R1b from Allentoft have been confirmed to be R1b1a2a2. So far Bell Beaker R1b is 2/2 R1b1a2a1a-P312(one is confirmed U152) from Haak and Allentoft.

Actually it's pretty simple. And those tools let you do it from a windows computer, which is usually the problem with people less familiar with unix systems. You do have to use the command line and understand if there is an error, but you can just Google all that and have answers in seconds.

I once sat through a class of uninterested bioinformatics students who basically re-assembled their own human genomes on their laptops. And that was several years ago.

to be a cracked record again if part of the R1b expansion was small groups like the African blacksmith guilds but connected to copper working rather than iron then they could potentially move very far relatively fast because they wouldn't have had to fight their way from A to B - just hop from trade node to trade node.

http://en.wikipedia.org/wiki/Blacksmiths_of_western_Africa

if so you might find little clusters of R1b anywhere there was ancient copper

(and if they'd originally come from the southern Urals they might have a cluster of red hair genes also)

From the data and the conclusions from the paper, it looks like the R1b pocket in Armenia is an outlier from the Yamna and European shared "Caucasus" ancestry. This indicates there was an eastern side expansion around the Caspian to Armenian highlands which is independent from any western expansions. I believe another wave of R1b-L23(xL51) is from a western expansion around the Black Sea and settled in southern Balkans (Greece/Albania) and Anatolia. Unfortunately we need more data to support this. In turn I believe Austria-Hungary is the birth place and/or bifurcation of L51+, and we see the remaining western expansions descend from this clade with "Western" IE speakers. We need to see more R1b SNP results to support this claim.

The relationship of Sintashta with the EEF admixed Corded people is fascinating. By the way, the Russian anthropologist V.V. Bunak has noted long before that the physical type of the Srubna culture differs quite a lot from the earlier Yamnaya and Catacomb people. The Srubna type resembles the modern central Russians and has smaller absolute measurements than the earlier steppe cultures. This is probably a consequence of EEF admixture. And of course, Srubna being dated to 2000 BC - 1500 BC, it's contemporaneous with the adjacent Sintashta culture.

I find it strange that they didn't include published EHG genomes in their dataset. Instead they use MA-1 to calculate f3 stats for Yamnaya and then they wonder that the admixture signal for Armenian-like admixture is so weak...

From the data on the paper I've not been able to make much. All the formal stats provided are not too informative. And some genomes seem to be of low quality (the ones from Montenegro and Lithuania, apparently).

I'm most curious about the Sintashta genomes. They seem to be similar to CWC or Unetice, but I think there might be some interesting differences. From the Bronze Age Armenian samples I'm not sure what to think. They seem quite "eastern" (little affinity to both WHG and EEF), but it might be a wrong impression from those limited stats. Soon we'll find out.

Looking forward to seeing your analysis David, you have techniques at your disposal this paper doesn't and I'm sure you'll find new stuff.

Examining the D stats in their Supplementary Table 5 (http://www.nature.com/nature/journal/v522/n7555/extref/nature14507-s5.xlsx), just to explore:

For Sintashta

D(Yoruba,Malta;Sintashta,Pop) is positive for most populations. So Sintashta less related to Mal'ta. No significant stat for e.g. D(Yoruba,Malta;Sintashta,Bell Beaker) while D(Yoruba,Malta;Sintashta,Yamnaya) is D = 0.029, significant at Z=8.37.

D(Yoruba,hunterW;Sintashta,Pop) for Bronze Age Armenia is D = -0.039, significant at Z=-12.56 and for Yamnaya D=-0.0107527, Z=-3.54. So both of these indicate that Sintashta is closer to hunter W than either of these two.

Likewise for Neolithic Central European D=-0.0135, significant at Z=-3.54 and Bronze Age Corded Ware actually positive at D=0.0084, Z=2.60. So out of these 4, only Corded Ware is closer to hunterW than Sintashta.

D(Yoruba,neolC;Sintashta,Pop) gives Yamnaya D=-0.013 and Bronze Age Armenia D=-0.0009, so Sintashta is indeed closer to Neolithic Central Europeans than both of these (more marginally for brArmenia). Non-sig for Andronovo.

Seems all more consistent with the idea that at least some admixture into Sintashta came specifically from Bronze Age East-Central Europe and not Bronze Age West Asia (whether it also came from other places or not).

Another minor one - D(Yoruba,Ust-Ishim;Sintashta,Pop), they are all positive, except for Neolithic Hungarians whch is mildly negative at a non-significant level.

Which implies that Sintashta is less related to Ust Ishim than all other populations (including Neolithic Central Europe although those are non-significant) and more "basal Eurasian". Must be wrong somehow.

The Sintashta samples on the ADMIXTURE also show some strange purple African component, even at fairly high K. Not sure why that is.

For Bronze Age Armenians:

Trying to gauge Malta affinity for Bronze Age Armenia with the stat D(Yoruba,Malta;Bronze Age Armenia,Pop), I see the average of the Neolithic Hungarian and Central European populations for this stat is D=-0.0146 and Z=-3.50. So Bronze Age Armenians are closer to Malta than Neolithic Europeans.

At the same time, similar stats for Yamnaya is D=0.048 and Z=12.2, while for Corded Ware is D=0.28, Z=7.41 and Bell Beaker D=0.20 and Z=4.82.

So this implies the Bronze Age Armenia was not very high in Malta affinity, more comparable to Neolithic Europeans than Bronze Age Europeans who are quite a bit closer to Malta than BRArmenian.

To check out Neolithic European farmer affinity for Bronze Age Armenians D(Yoruba,NeolithicHungarian;BronzeAgeArmenian,Pop).

For Yamnaya the stat is D=-0.01378, Z=-5.388, so closer than Yamnaya. While for Andronovo, the stat is D=0.0033, Z=1.28, so more or less Andronovo is as close to Neolithic Hungarians as Bronze Age Armenia. Corded Ware D=0.0106,Z=4.496 and Bell Beaker D=0.172,Z=6.566, so both of these populations are closer to Neolithic Hungarians than Bronze Age Armenians.

Finally hunterW D=0.0131, Z=4.20, so Western European hunter gatherers are closer to Neolithic Hungarians than Bronze Age Armenians are.

You'd Bronze Age Armenian expect them to have high f3 with Lezgins, who are the most similar to them on the the SI ADMIXTURE from Allentoft.

But no. For modern populations, its Scottish, Icelandic, Estonian, Lithuanian. Although Abkhazians and Georgians are relatively high up there as well, as are Corded Ware and Croatians. All with roughly comparable levels of SNPs.

Not much of what we'd expect as a simple regional pattern. And the f3 is pretty low for everyone.

Instead, a pattern a little akin to some of the Bell Beaker David's previous posted f3 stats for, where IIRC there was a dual affinity to both Basques and Lithuanians (which is present, but reduced in the Bell Beaker f3 stat here as well).

The 20% North European is mostly WHG. Thats the weird part. The sample has like 10% ANE and 20% WHG. 4 times! as much WHG as modern populations in the same region.

Also the ENF is Atlantic_Med which points that this can't have come from the Steppes, because those "lacked" Atlantic_Med.

It seems to be the remnant of early farmers.

As said dozen times. It really seems when the Semites (especially Assyrians) expanded they significantly changed the genetic make up of the region, by bringing a Red Sea like component from the Proto Afro_Asian homeland in Egypt. This probably gave birht to "Southwest Asian".

@KurtiIf the BA Armenians have no Southwest Asian component, in contrast to modern Armenian, that is surely a major result! It would make sense of the Assyrians brought Levantine and Arabian Peninsula populations into the Armenian area. They did have interactions with the Uratian/Lan Van populations during the acme of their hegemony.

According to Richard Rocca another Bell Beaker has come out R1b-P312+. This time it isn't U152, it's Z196+. Z196 is a widespread and popular subclade of DF27!! If DF27 was already in Germany over 4,000 years ago, that can explain it's widespread distribution today.

Richard Rocca. Anthrogencia. "German Bell Beaker sample SAMEA3325421 is P312+, but also Z196+, meaning he is also DF27. What is surprising however is that he is also Z195-. I don't think we have any modern Z196+Z195- samples, but I could be wrong. This of course could be huge for R1b!"

Interesting that U152 is 50% (2/4) of the northeastern Alpine EBA samples we have, and is also absent in the Remedello samples. Modern day, U152 is far more common in northwestern Italy than it is northeast of the Alps. Certainly makes me wonder how and when that happened.

1) Archaeologically: the Bronze Age was a low population, pastoral -type economy in much of Italy - esp north. Perhaps this is when pastroalist, R1b-bearers entered. The Iron Age saw rapid rise in population = ? consolidation

2)Working backwards, one can collate all the R1b groups from Italy (eg look at ftDNA), and do variance and age-estimations within italy, and compare it to other regions. Admittedly post-Hoc, it can give some clues until we see BA & IA samples from Italy.

No i mean't the Mutation is Ancestral to both European Z-280 and Asian Z-93, Yes Z-280 is European but Z-93 is also Asian, so we can assume people with such Ancestral mutation lived in Central Asia at least due to the lack of sampling from other parts of Asia...

David, Yes but certainly we have to see before we can judge and it will be interesting also to see if R1a-M417 Appears in other parts of Asia or not before the 2000 BC Period, i'm certain it will be there in Indus Valley but we have to wait.

But what I don't understand how did they even come to think this is "identical" to modern Armenians? This particular result here looks more Iranian than anything and is even slightly more eastern and less Southern(Southwest Asian) shifted than modern Iranians!

It seems more likely that Yamnaya near the Caspian carried almost exclusively R1b.

On the other hand, R1a was found among steppe groups that expanded into their territory from the west towards the end of the Early Bronze Age. Here's a quote from the Allentoft et al. paper.

"From the beginning of 2000 BC, a new class of master artisans known as the Sintashta culture emerged in the Urals, building chariots, breeding and training horses (Fig. 1), and producing sophisticated new weapons. These innovations quickly spread across Europe and into Asia where they appeared to give rise to the Andronovo culture19,20 (Fig. 1)."

It's hard to say what happened to the descendants of the eastern Yamnaya people at this time. Some were probably incorporated into the ranks of these newcomers, while others might have migrated out in a hurry. In any case, what we might be looking at here is a major ass whooping that forced R1b to rush out of the steppe.

The single Corded Ware R1b is confirmed to be R1b1a2a-L23, but he is negative for Eastern-branch Z2103 and western PF6543(parallel to L11). Although he wasn't tested for the ancestor of L11: L51. There was a R1b-L23* from Samara Yamanya, and I'm pretty sure it's found in Europe and West Asia today, but I don't know much about it's modern distribution.

Anyways, this Corded Ware R1b is older than any Bell Beaker R1bs. It's from 2880-2630BC, before Bell Beaker was in Germany. So, this is big news for Western European-R1b. It's evidence that Bell Beaker-itself is the not the source of R1b-L11, but that R1b was introduced to Bell Beaker by Eastern European immigrants.

The I2s and G2as continuously coming from EEF-like people(Italy, Hungary, in Allentoft) puts nail on the coffin for the idea R1b-L11 developed way way back in the middle of West Europe.

"Anyways, this Corded Ware R1b is older than any Bell Beaker R1bs. It's from 2880-2630BC, before Bell Beaker was in Germany. So, this is big news for Western European-R1b. It's evidence that Bell Beaker-itself is the not the source of R1b-L11, but that R1b was introduced to Bell Beaker by Eastern European immigrants."

I think that with modern calculators we might be seeing a lot of artefacts because of a not too high coverage genome and because of an unusually high (by modern standards) amounts of ANE. I would wait for David's analysis to have a better understanding of them.

Also, Kurti, it should be safe to consider that these people were recent arrivals to the area, so it doesn't necessarily mean that SW Asian was not present in the area before; rather that these newcomers didn't get it yet.

Soon we'll know, but to me these Armenians look quite "eastern", but not too "northern" (maybe some Lezgin-Tajik type, though too risky to say right now).

//a new class of master artisans known as the Sintashta culture emerged in the Urals, building chariots, breeding and training horses (Fig. 1), and producing sophisticated new weapons.//They obviously came from South i.e. BMAC.

Less ANE and WHG and more ENF than modern Scandinavians. Score is most similar to North Sea in general, and if anything closest to the British isles, North Netherlands and Germany. Very similar to German Bell Beaker and Unetice, and obviously differnt from German Corded Ware(Scandinavian Corded Ware?).